BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 027718
(219 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3PUF|A Chain A, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|D Chain D, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|G Chain G, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|J Chain J, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|M Chain M, Crystal Structure Of Human Rnase H2 Complex
pdb|3PUF|P Chain P, Crystal Structure Of Human Rnase H2 Complex
Length = 302
Score = 209 bits (531), Expect = 1e-54, Method: Compositional matrix adjust.
Identities = 97/189 (51%), Positives = 128/189 (67%)
Query: 13 NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN 72
PC++G+DEAGRGPVLGPMVY YCP L L ADSKTL E +RE LF ++
Sbjct: 30 EPCVLGVDEAGRGPVLGPMVYAICYCPLPRLADLEALKVADSKTLLESERERLFAKMEDT 89
Query: 73 DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
D VGWA+D++ P +S ML + K NLN +SHD+A GLI L+ G+ +T+V++DTVG
Sbjct: 90 DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMP 149
Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
E YQA+L Q FP I+ V KAD+LYPVVS ASI AKV RD+ ++ W F E +++ ++
Sbjct: 150 ETYQARLQQSFPGIEVTVKAKADALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDY 209
Query: 193 GSGYPGGAR 201
GSGYP +
Sbjct: 210 GSGYPNDPK 218
>pdb|3P5J|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
Length = 301
Score = 206 bits (524), Expect = 9e-54, Method: Compositional matrix adjust.
Identities = 97/189 (51%), Positives = 129/189 (68%), Gaps = 1/189 (0%)
Query: 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN- 72
PC++G+DEAGRGPVLGPMVY YCP S L L ADSKTL E +RE LF ++ +
Sbjct: 28 PCVLGVDEAGRGPVLGPMVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKMEEDG 87
Query: 73 DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
D VGWA+D++ P +S ML + K NLN +SHD+A GLI L+ + +T+V++DTVG
Sbjct: 88 DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGMP 147
Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
E YQA+L Q FP I+ V KADSL+PVVS ASI AKV RD+ ++ W F E +++ ++
Sbjct: 148 ETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDY 207
Query: 193 GSGYPGGAR 201
GSGYP +
Sbjct: 208 GSGYPNDPK 216
>pdb|3P56|A Chain A, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
pdb|3P56|D Chain D, The Structure Of The Human Rnase H2 Complex Defines Key
Interaction Interfaces Relevant To Enzyme Function And
Human Disease
Length = 299
Score = 203 bits (516), Expect = 7e-53, Method: Compositional matrix adjust.
Identities = 95/189 (50%), Positives = 126/189 (66%)
Query: 13 NPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN 72
PC++G+ EAGRGPVLGPMVY YCP L L ADSKTL E +RE LF ++
Sbjct: 27 EPCVLGVAEAGRGPVLGPMVYAICYCPLPRLADLEALKVADSKTLLESERERLFAKMEDT 86
Query: 73 DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
D VGWA+D++ P +S ML + K NLN +SHD+A GLI L+ G+ +T+V++DTVG
Sbjct: 87 DFVGWALDVLSPNLISTSMLGRVKYNLNSLSHDTATGLIQYALDQGVNVTQVFVDTVGMP 146
Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
E YQA+L Q FP I+ V KA +LYPVVS ASI AKV RD+ ++ W F E +++ ++
Sbjct: 147 ETYQARLQQSFPGIEVTVKAKAAALYPVVSAASICAKVARDQAVKKWQFVEKLQDLDTDY 206
Query: 193 GSGYPGGAR 201
GSGYP +
Sbjct: 207 GSGYPNDPK 215
>pdb|3KIO|A Chain A, Mouse Rnase H2 Complex
Length = 301
Score = 200 bits (509), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 95/189 (50%), Positives = 126/189 (66%), Gaps = 1/189 (0%)
Query: 14 PCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVN- 72
PC++G+DEAGRGPVLGP VY YCP S L L ADSKTL E +RE LF + +
Sbjct: 28 PCVLGVDEAGRGPVLGPXVYAICYCPLSRLADLEALKVADSKTLTENERERLFAKXEEDG 87
Query: 73 DSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDA 132
D VGWA+D++ P +S L + K NLN +SHD+A GLI L+ + +T+V++DTVG
Sbjct: 88 DFVGWALDVLSPNLISTSXLGRVKYNLNSLSHDTAAGLIQYALDQNVNVTQVFVDTVGXP 147
Query: 133 EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
E YQA+L Q FP I+ V KADSL+PVVS ASI AKV RD+ ++ W F E +++ ++
Sbjct: 148 ETYQARLQQHFPGIEVTVKAKADSLFPVVSAASIFAKVARDKAVKNWQFVENLQDLDSDY 207
Query: 193 GSGYPGGAR 201
GSGYP +
Sbjct: 208 GSGYPNDPK 216
>pdb|1IO2|A Chain A, Crystal Structure Of Type 2 Ribonuclease H From
Hyperthermophilic Archaeon, Thermococcus Kodakaraensis
Kod1
Length = 213
Score = 90.1 bits (222), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 70/204 (34%), Positives = 103/204 (50%), Gaps = 21/204 (10%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
I GIDEAGRGPV+GPMV + + L L DSK L ++RE+LF N+ +
Sbjct: 3 IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLF-----NEIL 57
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVG-DAE 133
G D + EL ++ + LNE ++ + LN + + +Y D D E
Sbjct: 58 GVLDDYV-ILELPPDVIGSREGTLNEFEVEN----FAKALNSLKVKPDVIYADAADVDEE 112
Query: 134 KYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR + E + +
Sbjct: 113 RFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV------EKLKEEYGEI 166
Query: 193 GSGYPGGARCLKLSIVCNNFQSFG 216
GSGYP R + + N ++ G
Sbjct: 167 GSGYPSDPRT--RAFLENYYREHG 188
>pdb|1X1P|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-197)-A(28-42)
Length = 212
Score = 90.1 bits (222), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 68/190 (35%), Positives = 97/190 (51%), Gaps = 19/190 (10%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
I GIDEAGRGPV+GPMV + + L L DSK L ++RE+LF N+ +
Sbjct: 3 IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLF-----NEIL 57
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVG-DAE 133
G D + EL ++ + LNE ++ + LN + + +Y D D E
Sbjct: 58 GVLDDYV-ILELPPDVIGSREGTLNEFEVEN----FAKALNSLKVKPDVIYADAADVDEE 112
Query: 134 KYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR + E + +
Sbjct: 113 RFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV------EKLKEEYGEI 166
Query: 193 GSGYPGGARC 202
GSGYP R
Sbjct: 167 GSGYPSDPRT 176
>pdb|2DFE|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-200)-C
Length = 209
Score = 89.7 bits (221), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 68/190 (35%), Positives = 97/190 (51%), Gaps = 19/190 (10%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
I GIDEAGRGPV+GPMV + + L L DSK L ++RE+LF N+ +
Sbjct: 3 IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLF-----NEIL 57
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVG-DAE 133
G D + EL ++ + LNE ++ + LN + + +Y D D E
Sbjct: 58 GVLDDYV-ILELPPDVIGSREGTLNEFEVEN----FAKALNSLKVKPDVIYADAADVDEE 112
Query: 134 KYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR + E + +
Sbjct: 113 RFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV------EKLKEEYGEI 166
Query: 193 GSGYPGGARC 202
GSGYP R
Sbjct: 167 GSGYPSDPRT 176
>pdb|2DFH|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-212)-C
Length = 221
Score = 89.7 bits (221), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 68/190 (35%), Positives = 97/190 (51%), Gaps = 19/190 (10%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
I GIDEAGRGPV+GPMV + + L L DSK L ++RE+LF N+ +
Sbjct: 3 IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLF-----NEIL 57
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVG-DAE 133
G D + EL ++ + LNE ++ + LN + + +Y D D E
Sbjct: 58 GVLDDYV-ILELPPDVIGSREGTLNEFEVEN----FAKALNSLKVKPDVIYADAADVDEE 112
Query: 134 KYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR + E + +
Sbjct: 113 RFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV------EKLKEEYGEI 166
Query: 193 GSGYPGGARC 202
GSGYP R
Sbjct: 167 GSGYPSDPRT 176
>pdb|2DFF|A Chain A, Crystal Structure Of Tk-Rnase Hii(1-204)-C
Length = 213
Score = 89.7 bits (221), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 68/190 (35%), Positives = 97/190 (51%), Gaps = 19/190 (10%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
I GIDEAGRGPV+GPMV + + L L DSK L ++RE+LF N+ +
Sbjct: 3 IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLF-----NEIL 57
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLN-IGILLTEVYLDTVG-DAE 133
G D + EL ++ + LNE ++ + LN + + +Y D D E
Sbjct: 58 GVLDDYV-ILELPPDVIGSREGTLNEFEVEN----FAKALNSLKVKPDVIYADAADVDEE 112
Query: 134 KYQAKLSQRFPSIKFVVSK-KADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
++ +L +R VV+K KAD ++PVVS ASI+AKVTRDR + E + +
Sbjct: 113 RFARELGERLNFEAEVVAKHKADDIFPVVSAASILAKVTRDRAV------EKLKEEYGEI 166
Query: 193 GSGYPGGARC 202
GSGYP R
Sbjct: 167 GSGYPSDPRT 176
>pdb|1EKE|A Chain A, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii)
With Mes Ligand
pdb|1EKE|B Chain B, Crystal Structure Of Class Ii Ribonuclease H (Rnase Hii)
With Mes Ligand
Length = 230
Score = 87.4 bits (215), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 70/205 (34%), Positives = 106/205 (51%), Gaps = 29/205 (14%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
I+GIDEAGRGPVLGP V ++ L L DSK L + KR L K+ +++
Sbjct: 3 IIGIDEAGRGPVLGPXVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYL---KKLLENL 59
Query: 76 GWAVDIIDPRELSAKMLNK--NKINLNEISHDS----AIGLITRVLNIGILLTEVYLDTV 129
G+ ++ R L A+ +N+ N INLN+I ++ A LI + LNI E+Y+D
Sbjct: 60 GY----VEKRILEAEEINQLXNSINLNDIEINAFSKVAKNLIEK-LNIRDDEIEIYIDAC 114
Query: 130 GD---------AEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWI 180
+K + + +R +IK + KAD+ YPVVS ASI+AK RD + +
Sbjct: 115 STNTKKFEDSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYY- 173
Query: 181 FEETAENMHRNFGSGYPGGARCLKL 205
+ ++ + GSGYP + +K
Sbjct: 174 -----KKIYGDIGSGYPSDPKTIKF 193
>pdb|1UAX|A Chain A, Crystal Structure Of The Ribonuclease H2 From Pyrococcus
Horikoshii Ot3
pdb|1UAX|B Chain B, Crystal Structure Of The Ribonuclease H2 From Pyrococcus
Horikoshii Ot3
Length = 220
Score = 83.2 bits (204), Expect = 9e-17, Method: Compositional matrix adjust.
Identities = 59/191 (30%), Positives = 96/191 (50%), Gaps = 21/191 (10%)
Query: 16 IMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
+ G+DEAGRGPV+GP+V G + L + DSK L +RE+LF L ++
Sbjct: 3 VAGVDEAGRGPVIGPLVIGVAVIDEKNIERLRDIGVKDSKQLTPGQREKLFSKL-IDILD 61
Query: 76 GWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEKY 135
+ V ++ P+E+ + + N++ A + + ++ I ++Y+D+ K
Sbjct: 62 DYYVLLVTPKEIDERHHSMNELE--------AEKFVVALNSLRIKPQKIYVDSADVDPKR 113
Query: 136 QAKLSQRFPSIKF----VVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRN 191
A L + +K+ + KAD+ Y +VS ASI+AKVTRDR + E + +
Sbjct: 114 FASLIK--AGLKYEATVIAEHKADAKYEIVSAASIIAKVTRDREI------EKLKQKYGE 165
Query: 192 FGSGYPGGARC 202
FGSGYP R
Sbjct: 166 FGSGYPSDPRT 176
>pdb|3P83|D Chain D, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|E Chain E, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus.
pdb|3P83|F Chain F, Structure Of The Pcna:rnase Hii Complex From Archaeoglobus
Fulgidus
Length = 217
Score = 76.6 bits (187), Expect = 9e-15, Method: Compositional matrix adjust.
Identities = 61/195 (31%), Positives = 94/195 (48%), Gaps = 20/195 (10%)
Query: 8 PKWASNPCIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFE 67
P++ GIDEAG+G V+GP+V + C S + L L DSK L + +REEL E
Sbjct: 6 PEFPGRLMKAGIDEAGKGCVIGPLVVAGVAC--SDEDRLRKLGVKDSKKLSQGRREELAE 63
Query: 68 DLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEV-YL 126
+++ V + P L +M K +NEI + +I R L E+ Y+
Sbjct: 64 EIR--KICRTEVLKVSPENLDERMAAKT---INEILKECYAEIILR------LKPEIAYV 112
Query: 127 DTVGDAEKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAE 186
D+ + ++ + ++ V KAD YP+V+ ASI+AKV R+R + E +
Sbjct: 113 DSPDVIPERLSRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREI------ERLK 166
Query: 187 NMHRNFGSGYPGGAR 201
+FGSGY R
Sbjct: 167 EKFGDFGSGYASDPR 181
>pdb|1I39|A Chain A, Rnase Hii From Archaeoglobus Fulgidus
pdb|1I3A|A Chain A, Rnase Hii From Archaeoglobus Fulgidus With Cobalt
Hexammine Chloride
Length = 225
Score = 76.6 bits (187), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 60/185 (32%), Positives = 91/185 (49%), Gaps = 20/185 (10%)
Query: 18 GIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVGW 77
GIDEAG+G V+GP+V + CS + L L DSK L + +REEL E+++
Sbjct: 24 GIDEAGKGCVIGPLVVAGV--ACSDEDRLRKLGVKDSKKLSQGRREELAEEIR--KICRT 79
Query: 78 AVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEV-YLDTVGDAEKYQ 136
V + P L +M K +NEI + +I R L E+ Y+D+ +
Sbjct: 80 EVLKVSPENLDERMAAKT---INEILKECYAEIILR------LKPEIAYVDSPDVIPERL 130
Query: 137 AKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGY 196
++ + ++ V KAD YP+V+ ASI+AKV R+R + E + +FGSGY
Sbjct: 131 SRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREI------ERLKEKFGDFGSGY 184
Query: 197 PGGAR 201
R
Sbjct: 185 ASDPR 189
>pdb|3O3G|A Chain A, T. Maritima Rnase H2 In Complex With Nucleic Acid
Substrate And Calcium Ions
Length = 222
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 46/182 (25%), Positives = 82/182 (45%), Gaps = 31/182 (17%)
Query: 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
+ G+DEAGRG + GP+V ++ + +N DSK L KRE L +++ +
Sbjct: 12 IVAGVDEAGRGCLAGPVV----AAAVVLEKEIEGIN--DSKQLSPAKRERLLDEIMEKAA 65
Query: 75 VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
VG + I P E I+L I + + + + + N+ + + V +D G
Sbjct: 66 VG--IGIASPEE----------IDLYNIFNATKLAMNRALENLSVKPSFVLVDGKG---- 109
Query: 135 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGW--IFEETAENMHRNF 192
+ P V K D ++ ASIVAKV RDR + + ++ + + + H+ +
Sbjct: 110 ----IELSVPGTCLV---KGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGY 162
Query: 193 GS 194
+
Sbjct: 163 AT 164
>pdb|2D0A|A Chain A, Crystal Structure Of Bst-Rnase Hiii
pdb|2D0B|A Chain A, Crystal Structure Of Bst-Rnase Hiii In Complex With Mg2+
pdb|2D0C|A Chain A, Crystal Structure Of Bst-Rnase Hiii In Complex With Mn2+
Length = 310
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 48/188 (25%), Positives = 80/188 (42%), Gaps = 17/188 (9%)
Query: 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVG 76
+G DE G G GP+V Y + +A L DSK L +E + + + ++V
Sbjct: 94 IGSDEVGTGDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAIKRIAP--AIMETVP 151
Query: 77 WAVDIID-PRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTE-VYLDTVGDAEK 134
AV ++D P+ + + + + H+ L+ V I E + +D +
Sbjct: 152 HAVTVLDNPQYNRWQRSGMPQTKMKALLHNRT--LVKLVDAIAPAEPEAIIIDEFLKRDS 209
Query: 135 YQAKLSQRFPSIKFVVS--KKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
Y LS I+ V KA+S++ V+ ASI+A+ ++F E E + R
Sbjct: 210 YFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIAR---------YVFLEEMEQLSRAV 260
Query: 193 GSGYPGGA 200
G P GA
Sbjct: 261 GLLLPKGA 268
>pdb|3ASM|A Chain A, Crystal Structure Of Q54a Mutant Protein Of Bst-Rnase Hiii
Length = 310
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 48/188 (25%), Positives = 80/188 (42%), Gaps = 17/188 (9%)
Query: 17 MGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSVG 76
+G DE G G GP+V Y + +A L DSK L +E + + + ++V
Sbjct: 94 IGSDEVGTGDYFGPIVVAAAYVDRPHIAKIAALGVKDSKQLNDEAIKRIAP--AIMETVP 151
Query: 77 WAVDIID-PRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTE-VYLDTVGDAEK 134
AV ++D P+ + + + + H+ L+ V I E + +D +
Sbjct: 152 HAVTVLDNPQYNRWQRSGMPQTKMKALLHNRT--LVKLVDAIAPAEPEAIIIDEFLKRDS 209
Query: 135 YQAKLSQRFPSIKFVVS--KKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 192
Y LS I+ V KA+S++ V+ ASI+A+ ++F E E + R
Sbjct: 210 YFRYLSDEDRIIRERVHCLPKAESVHVSVAAASIIAR---------YVFLEEMEQLSRAV 260
Query: 193 GSGYPGGA 200
G P GA
Sbjct: 261 GLLLPKGA 268
>pdb|3O3F|A Chain A, T. Maritima Rnase H2 D107n In Complex With Nucleic Acid
Substrate And Magnesium Ions
pdb|3O3H|A Chain A, T. Maritima Rnase H2 D107n In Complex With Nucleic Acid
Substrate And Manganese Ions
Length = 222
Score = 40.0 bits (92), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 45/182 (24%), Positives = 82/182 (45%), Gaps = 31/182 (17%)
Query: 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
+ G+DEAGRG + GP+V ++ + +N DSK L KRE L +++ +
Sbjct: 12 IVAGVDEAGRGCLAGPVVA----AAVVLEKEIEGIN--DSKQLSPAKRERLLDEIMEKAA 65
Query: 75 VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
VG + I P E I+L I + + + + + N+ + + V ++ G
Sbjct: 66 VG--IGIASPEE----------IDLYNIFNATKLAMNRALENLSVKPSFVLVNGKG---- 109
Query: 135 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGW--IFEETAENMHRNF 192
+ P V K D ++ ASIVAKV RDR + + ++ + + + H+ +
Sbjct: 110 ----IELSVPGTCLV---KGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGY 162
Query: 193 GS 194
+
Sbjct: 163 AT 164
>pdb|2ETJ|A Chain A, Crystal Structure Of Ribonuclease Hii (ec 3.1.26.4) (rnase
Hii) (tm0915) From Thermotoga Maritima At 1.74 A
Resolution
Length = 250
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 45/160 (28%), Positives = 70/160 (43%), Gaps = 29/160 (18%)
Query: 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
+ G+DEAGRG + GP+V ++ + +N DSK L KRE L +++ +
Sbjct: 25 IVAGVDEAGRGCLAGPVVAAA----VVLEKEIEGIN--DSKQLSPAKRERLLDEIXEKAA 78
Query: 75 VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
VG + I P E I+L I + + + + N+ + + V +D G
Sbjct: 79 VG--IGIASPEE----------IDLYNIFNATKLAXNRALENLSVKPSFVLVDGKG---- 122
Query: 135 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDR 174
+ P V K D ++ ASIVAKV RDR
Sbjct: 123 ----IELSVPGTCLV---KGDQKSKLIGAASIVAKVFRDR 155
>pdb|4HHT|A Chain A, T. Maritima Rnase H2 G21s In Complex With Nucleic Acid
Substrate And Calcium Ions
Length = 237
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 45/182 (24%), Positives = 81/182 (44%), Gaps = 31/182 (17%)
Query: 15 CIMGIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLKVNDS 74
+ G+DEA RG + GP+V ++ + +N DSK L KRE L +++ +
Sbjct: 12 IVAGVDEASRGCLAGPVVAAA----VVLEKEIEGIN--DSKQLSPAKRERLLDEIMEKAA 65
Query: 75 VGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTEVYLDTVGDAEK 134
VG + I P E I+L I + + + + + N+ + + V +D G
Sbjct: 66 VG--IGIASPEE----------IDLYNIFNATKLAMNRALENLSVKPSFVLVDGKG---- 109
Query: 135 YQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGW--IFEETAENMHRNF 192
+ P V K D ++ ASIVAKV RDR + + ++ + + + H+ +
Sbjct: 110 ----IELSVPGTCLV---KGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGY 162
Query: 193 GS 194
+
Sbjct: 163 AT 164
>pdb|3VN5|A Chain A, Crystal Structure Of Aquifex Aeolicus Rnase H3
Length = 257
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 31/53 (58%)
Query: 18 GIDEAGRGPVLGPMVYGCLYCPCSYQQTLATLNFADSKTLKEEKREELFEDLK 70
G DE+G+G + G +V C+ P +++LN D+K L +++ E L+ LK
Sbjct: 75 GCDESGKGDIFGSLVLCCVCIPEENYLKVSSLNPRDTKRLSDKRVERLYLALK 127
>pdb|2FJA|A Chain A, Adenosine 5'-Phosphosulfate Reductase In Complex With
Substrate
pdb|2FJA|C Chain C, Adenosine 5'-Phosphosulfate Reductase In Complex With
Substrate
pdb|2FJB|A Chain A, Adenosine-5'-Phosphosulfate Reductase Im Complex With
Products
pdb|2FJB|C Chain C, Adenosine-5'-Phosphosulfate Reductase Im Complex With
Products
pdb|2FJD|A Chain A, Adenosine-5-Phosphosulfate Reductase In Complex With
Sulfite (Covalent Adduct)
pdb|2FJD|C Chain C, Adenosine-5-Phosphosulfate Reductase In Complex With
Sulfite (Covalent Adduct)
pdb|2FJE|A Chain A, Adenosine-5-Phosphosulfate Reductase Oxidized State
pdb|2FJE|C Chain C, Adenosine-5-Phosphosulfate Reductase Oxidized State
Length = 643
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 43 QQTLATLNFADSKTLKE--EKREELFEDLKVNDSVGWAVDIIDPRE 86
++ LA L D K LK E+ E F D+ V+ ++ WA IDP+E
Sbjct: 337 EEALAELAGGDKKKLKHIYEEAFEDFLDMTVSQALLWACQNIDPQE 382
>pdb|1JNR|A Chain A, Structure Of Adenylylsulfate Reductase From The
Hyperthermophilic Archaeoglobus Fulgidus At 1.6
Resolution
pdb|1JNR|C Chain C, Structure Of Adenylylsulfate Reductase From The
Hyperthermophilic Archaeoglobus Fulgidus At 1.6
Resolution
pdb|1JNZ|A Chain A, Structure Of Adenylylsulfate Reductase From The
Hyperthermophilic Archaeoglobus Fulgidus At 1.6
Resolution
pdb|1JNZ|C Chain C, Structure Of Adenylylsulfate Reductase From The
Hyperthermophilic Archaeoglobus Fulgidus At 1.6
Resolution
Length = 643
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 2/46 (4%)
Query: 43 QQTLATLNFADSKTLKE--EKREELFEDLKVNDSVGWAVDIIDPRE 86
++ LA L D K LK E+ E F D+ V+ ++ WA IDP+E
Sbjct: 337 EEALAELAGGDKKKLKHIYEEAFEDFLDMTVSQALLWACQNIDPQE 382
>pdb|2ZME|B Chain B, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 238
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 12/98 (12%)
Query: 55 KTLKEEKRE------ELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAI 108
+ L+E+++E E FEDL + + ELS + NK K +I+ D I
Sbjct: 13 RKLEEKRKETDKNISEAFEDLS-----KLMIKAKEMVELSKSIANKIKDKQGDITEDETI 67
Query: 109 GLITRVLNIGILLTEVYLDTVGDAEKYQAKLSQRFPSI 146
+ +L++GI V +T G +Y +L+++ I
Sbjct: 68 RFKSYLLSMGI-ANPVTRETYGSGTQYHMQLAKQLAGI 104
>pdb|3MBI|A Chain A, Crystal Structure Of The Phosphoribosylpyrophosphate
(Prpp) Synthetase From Thermoplasma Volcanium In Complex
With Adp-Mg2+ And Ribose 5- Phosphate
pdb|3MBI|B Chain B, Crystal Structure Of The Phosphoribosylpyrophosphate
(Prpp) Synthetase From Thermoplasma Volcanium In Complex
With Adp-Mg2+ And Ribose 5- Phosphate
pdb|3MBI|C Chain C, Crystal Structure Of The Phosphoribosylpyrophosphate
(Prpp) Synthetase From Thermoplasma Volcanium In Complex
With Adp-Mg2+ And Ribose 5- Phosphate
pdb|3MBI|D Chain D, Crystal Structure Of The Phosphoribosylpyrophosphate
(Prpp) Synthetase From Thermoplasma Volcanium In Complex
With Adp-Mg2+ And Ribose 5- Phosphate
Length = 287
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 40 CSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
SY ++AT++ D KTL K + F DL ND++
Sbjct: 114 SSYSNSIATVDIHDEKTLSYSKVK--FSDLHANDAI 147
>pdb|3LPN|A Chain A, Crystal Structure Of The Phosphoribosylpyrophosphate
(Prpp) Synthetase From Thermoplasma Volcanium In Complex
With An Atp Analog (Ampcpp).
pdb|3LPN|B Chain B, Crystal Structure Of The Phosphoribosylpyrophosphate
(Prpp) Synthetase From Thermoplasma Volcanium In Complex
With An Atp Analog (Ampcpp).
pdb|3LRT|A Chain A, Crystal Structure Of The Phosphoribosyl Pyrophosphate
(Prpp) Synthetase From Thermoplasma Volcanium In Complex
With Adp.
pdb|3LRT|B Chain B, Crystal Structure Of The Phosphoribosyl Pyrophosphate
(Prpp) Synthetase From Thermoplasma Volcanium In Complex
With Adp.
pdb|3NAG|A Chain A, Crystal Structure Of The Phosphoribosylpyrophosphate
(Prpp) Synthetase From Thermoplasma Volcanium In Complex
With Adp
pdb|3NAG|B Chain B, Crystal Structure Of The Phosphoribosylpyrophosphate
(Prpp) Synthetase From Thermoplasma Volcanium In Complex
With Adp
Length = 286
Score = 28.5 bits (62), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 40 CSYQQTLATLNFADSKTLKEEKREELFEDLKVNDSV 75
SY ++AT++ D KTL K + F DL ND++
Sbjct: 112 SSYSNSIATVDIHDEKTLSYSKVK--FSDLHANDAI 145
>pdb|3CUQ|B Chain B, Integrated Structural And Functional Model Of The Human
Escrt-Ii Complex
Length = 218
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 6/83 (7%)
Query: 64 ELFEDLKVNDSVGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLTE 123
E FEDL + + ELS + NK K +I+ D I + +L++GI
Sbjct: 8 EAFEDLS-----KLMIKAKEMVELSKSIANKIKDKQGDITEDETIRFKSYLLSMGI-ANP 61
Query: 124 VYLDTVGDAEKYQAKLSQRFPSI 146
V +T G +Y +L+++ I
Sbjct: 62 VTRETYGSGTQYHMQLAKQLAGI 84
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.319 0.136 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,335,079
Number of Sequences: 62578
Number of extensions: 238010
Number of successful extensions: 621
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 577
Number of HSP's gapped (non-prelim): 33
length of query: 219
length of database: 14,973,337
effective HSP length: 95
effective length of query: 124
effective length of database: 9,028,427
effective search space: 1119524948
effective search space used: 1119524948
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)